You should not much trust on link building software while Google now updating continually search strategy, like panda penguin updates. This type link building practices Can Hurt Your Google Rankings.

SEO Spyglass is a common one. Open Site Explorer is also worth checking. Doesnt matter what one you end up using though, only a portion of backlinks show up.

Ahrefs & Majestic SEO.

Ahrefs is easily my favorite. You can get up to 15 requests a day with a free account. If you need more, just pay for an account.

If you can deal with the annoying pop-ups, backlinkwatch.com is a good web-based service which is free.

Hy Fellas, I think SEO Power Suite is one the best free tools. I have been using it for a long...
Thanks

Different link checkers give different data, so you need an effective link checker which you trust.

All these can be discovered in WebMeUp, even though the tool is more of a package solution. Сompetition analysis is one of the most powerful modules in WebMeUp, while others are keywords and rankings, on-page analysis, backlinks, seo reporting..
In ‘Competitors’ module it is possible to analyze competition from all sides, including their linkbuilding activity, on-page optimization, keywords, link value, competitor’s most juicy links and so on.
The free trial of WebMeUp allows getting 25k links per competitor and analyze 10 competitors overall. And in the near future we’re planning to add a new backlink tool which will be unearthing 100k+ competitor backlinks per project.

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Backlinkwatch.com is a good one except those irritating pop-ups.
however majesticseo.com is the most reliable.

Also Google Webmaster Tools is the best amongst all, if you are checking your own site's backlinks. It provides you detailed information of all the links that point back to your site apart from some other useful statistics related to your site.

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